The judgement of TP between the vcf files using vcfeval. Are 0/1 and 1/0 the same by using rtg tools vcfeval

Question

[Lingwei]

Hi,

I was trying to do vcfeval to do the concordance between two vcf files. I think 0/1 and 1/0 would be the same. But I don't know how the vcfeval would do. Will they be treated as different? Does someone know that?

Thank you.

Answer 1

[4galaxy77]

If they are unphased (i.e. separated by a / rather than a |, which means they are reversible), then yes, they will be treated as the same.

[Lingwei]

Ok, thank you!